The COVID-19 pandemic has caused stress as well as modified physical activity and eating habits among university students. The objectives were to identify the changes in body mass index (BMI) and eating disorders among university students between 2009 and 2021. Between 2009 and 2021, five repeated cross-sectional studies were conducted among university students who filled in an anonymous online self-questionnaire. Age, gender, and BMI were recorded, and the SCOFF questionnaire was used for ED screening which, in combination with BMI, allows to identify the four broad categories of ED with the Expali algorithm. With the five studies, 8981 university students were included in total. Obesity steadily increased between 2009 and 2021, for both men and women. The prevalence of ED was stable between 2009 and 2018 and significantly increased from 31.8% in 2018 to 51.8% in 2021 for women (p trend < 0.0001), and from 13.0% in 2009 to 31.3% in 2021 for men (p trend < 0.0001). All types of ED increased significantly between 2009 and 2021, except for restrictive ED among men. These results indicate for the first time a significant increase in ED prevalence among students since the COVID-19 pandemic. Initiatives to reinforce early screening of ED to implement targeted interventions in the student population are urgently needed.